Fixes Open-Systems-Pharmacology#356 display minor ticks (Open-Systems…

…-Pharmacology#357)

* Fixes Open-Systems-Pharmacology#356 display minor ticks

* fix test

Co-authored-by: Indrajeet Patil <patilindrajeet.science@gmail.com>

R/plotconfiguration-axis.R

@@ -79,6 +79,7 @@ AxisConfiguration <- R6::R6Class(
     #' Use enum `Scaling` to access predefined scales.
     #' @param ticks numeric vector or function defining where to position axis ticks
     #' @param ticklabels character vector or function defining what to print on axis ticks
+    #' @param minorTicks numeric vector or function defining where to position minor axis ticks
     #' @param font `Font` object defining the font of ticklabels
     #' @param expand logical defining if data is expanded until axis.
     #' If `TRUE`, data is expanded until axis
@@ -88,6 +89,7 @@ AxisConfiguration <- R6::R6Class(
                           scale = Scaling$lin,
                           ticks = NULL,
                           ticklabels = NULL,
+                          minorTicks = NULL,
                           font = NULL,
                           expand = FALSE) {
       validateIsNumeric(limits, nullAllowed = TRUE)
@@ -99,6 +101,7 @@ AxisConfiguration <- R6::R6Class(
       private$.scale <- .createPlotScale(scale)
       private$.ticks <- .createPlotTicks(ticks)
       private$.ticklabels <- .createPlotTickLabels(ticklabels)
+      private$.minorTicks <- .createPlotTicks(minorTicks)
       private$.expand <- expand
 
       # Default axis font will use theme
@@ -147,6 +150,21 @@ AxisConfiguration <- R6::R6Class(
         private$.ticks
       )
     },
+
+    #' @description Get tick values for pretty default log plots
+    #' @return User defined tick values or tlf default ticks
+    prettyMinorTicks = function() {
+      # A waiver is a ggplot2 "flag" object, similar to NULL,
+      # that indicates the calling function should just use the default value
+      if (!isOfType(private$.minorTicks, "waiver")) {
+        return(private$.minorTicks)
+      }
+      # Default tick values as a function of scale
+      if(isIncluded(private$.scale, Scaling$log)){
+        return(tlfEnv$logMinorTicks)
+      }
+      return(private$.minorTicks)
+    },
 
     #' @description Get tick labels for pretty default log plots
     #' @return User defined tick labels or tlf default ticklabels
@@ -200,6 +218,14 @@ AxisConfiguration <- R6::R6Class(
       private$.ticks <- .createPlotTicks(value)
       return(invisible())
     },
+    #' @field minorTicks function or values defining where axis minor ticks are placed
+    minorTicks = function(value) {
+      if (missing(value)) {
+        return(private$.minorTicks)
+      }
+      private$.minorTicks <- .createPlotTicks(value)
+      return(invisible())
+    },
     #' @field ticklabels function or values defining the axis tick labels
     ticklabels = function(value) {
       if (missing(value)) {
@@ -243,6 +269,7 @@ AxisConfiguration <- R6::R6Class(
     .scale = NULL,
     .ticks = NULL,
     .ticklabels = NULL,
+    .minorTicks = NULL,
     .font = NULL,
     .expand = NULL
   )
@@ -286,6 +313,7 @@ XAxisConfiguration <- R6::R6Class(
           ggplot2::scale_x_continuous(
             trans = self$ggplotScale(),
             breaks = self$prettyTicks(),
+            minor_breaks = self$prettyMinorTicks(),
             labels = self$prettyTickLabels(),
             expand = self$ggplotExpansion(),
             oob = .removeInfiniteValues
@@ -344,6 +372,7 @@ YAxisConfiguration <- R6::R6Class(
           ggplot2::scale_y_continuous(
             trans = self$ggplotScale(),
             breaks = self$prettyTicks(),
+            minor_breaks = self$prettyMinorTicks(),
             labels = self$prettyTickLabels(),
             expand = self$ggplotExpansion(),
             oob = .removeInfiniteValues

R/plotconfiguration-background.R

@@ -53,7 +53,10 @@ BackgroundConfiguration <- R6::R6Class(
         axis.line.x = private$.xAxis$createPlotElement(),
         axis.line.y = private$.yAxis$createPlotElement(),
         panel.grid.major.x = private$.xGrid$createPlotElement(),
-        panel.grid.major.y = private$.yGrid$createPlotElement()
+        panel.grid.major.y = private$.yGrid$createPlotElement(),
+        # Minor grid is same as Major grid but less thick
+        panel.grid.minor.x = private$.xGrid$createPlotElement(size = as.numeric(private$.xGrid$size)/2),
+        panel.grid.minor.y = private$.yGrid$createPlotElement(size = as.numeric(private$.yGrid$size)/2)
       )
       return(plotObject)
     }

R/tlf-env.R

@@ -165,8 +165,10 @@ setDefaultWatermark <- function(watermark = NULL) {
   return(invisible())
 }
 
-tlfEnv$logTicks <- 10^seq(-6, 6)
-tlfEnv$lnTicks <- exp(seq(-6, 6))
+tlfEnv$logTicks <- 10^seq(-10, 10)
+tlfEnv$lnTicks <- exp(seq(-10, 10))
+# Log minor ticks for every integer
+tlfEnv$logMinorTicks <- rep(seq(1,9), 21)*rep(10^seq(-10, 10), each = 9)
 
 #' @title setDefaultLogTicks
 #' @description Set default values for log ticks

R/utilities-axis.R

@@ -5,6 +5,7 @@
 #' @param limits Optional numeric values of axis limits
 #' @param ticks Optional values or function for axis ticks
 #' @param ticklabels Optional values or function for axis ticklabels
+#' @param minorTicks Optional values or function for axis minor ticks
 #' @param font A `Font` object  defining font of ticklabels
 #' @param expand Logical defining if data is expanded until axis
 #' @return A `ggplot` object
@@ -28,6 +29,7 @@ setXAxis <- function(plotObject,
                      limits = NULL,
                      ticks = NULL,
                      ticklabels = NULL,
+                     minorTicks = NULL,
                      font = NULL,
                      expand = NULL) {
   validateIsOfType(plotObject, "ggplot")
@@ -43,7 +45,7 @@ setXAxis <- function(plotObject,
 
   # R6 class not cloned will spread modifications into newPlotObject$plotConfiguration$xAxis
   xAxis <- newPlotObject$plotConfiguration$xAxis
-  eval(.parseVariableToObject("xAxis", c("limits", "scale", "ticks", "ticklabels", "font", "expand"), keepIfNull = TRUE))
+  eval(.parseVariableToObject("xAxis", c("limits", "scale", "ticks", "ticklabels", "minorTicks", "font", "expand"), keepIfNull = TRUE))
   newPlotObject <- xAxis$updatePlot(newPlotObject, ylim = newPlotObject$plotConfiguration$yAxis$limits)
   return(newPlotObject)
 }
@@ -72,6 +74,7 @@ setYAxis <- function(plotObject,
                      limits = NULL,
                      ticks = NULL,
                      ticklabels = NULL,
+                     minorTicks = NULL,
                      font = NULL,
                      expand = NULL) {
   validateIsOfType(plotObject, "ggplot")
@@ -87,7 +90,7 @@ setYAxis <- function(plotObject,
 
   # R6 class not cloned will spread modifications into newPlotObject$plotConfiguration$yAxis
   yAxis <- newPlotObject$plotConfiguration$yAxis
-  eval(.parseVariableToObject("yAxis", c("limits", "scale", "ticks", "ticklabels", "font", "expand"), keepIfNull = TRUE))
+  eval(.parseVariableToObject("yAxis", c("limits", "scale", "ticks", "ticklabels", "minorTicks", "font", "expand"), keepIfNull = TRUE))
   newPlotObject <- yAxis$updatePlot(newPlotObject, xlim = newPlotObject$plotConfiguration$xAxis$limits)
   return(newPlotObject)
 }